Month: January 2011

I have a bad tendency in my research work to write my own code and libraries from scratch, in large part because I’ve decided to keep most of my coding in Common Lisp to leverage prior tools. However, I’ve recently been given a painful demonstration of how it is often faster to pay the up-front cost to learn the right tool than to rewrite (and maintain) the subsets you think you need. For example, I found myself venturing into Clojure/Java/Hadoop for my commercial work this year as a compromise between Lisp / dynamic language features and integration benefits. This week I’m finding the need to do some rather sophisticated work with graphical models and I need some tools to build and evaluate them.

I’ve looked at a wide variety of open source approaches such as Samiam (no continuous variables), WinBUGS (only windows), OpenBUGS (not quite ready), HBC (inference only), Mallett (OK, but I don’t like Java and doesn’t support all forms of real-valued random variables), Incanter (limited but growing support for graphical models) and R.

Self-tracking is a process through which we attempt to uncover patterns in our daily lives or environment. Tracking can be used for a variety of purposes, including exploratory (what correlations do I see), explanatory (why does this happen) or experimental (If I change X, Y should happen). Regardless of the specific purpose, our ultimate goal is almost always to develop some model of cause and effect that we can use to inform our future decisions. The discovery of cause-effect relationships and the consequences of interventions is the essential aim of the scientific method. It takes years of education and practical training to understand how to apply methodology to gain valid insights into fundamental questions about cause and effect in some natural or artificial system. Methodology is crucial to avoid developing incorrect conclusions.

I’m looking forward to spending the next few days with the Lybba team. Lybba is a fantastic non-profit organization doing important work to transform the way that we interact with our individual health and the healthcare system.

I had a great time giving an unusual talk at the Quantified Selfmeetup in SF last week. Several people asked me to post slides online. There were also a few questions we didn’t have time to address to which this is a partial answer.

Self-Experimentation without a Written Record

Tracking my lifestyle changes and related symptoms on an ongoing basis has proved to be challenging. The severity of my symptoms have never been such that I’ve made detailed note-taking a priority. Instead, I slowly evolved a mental methodology for keeping track of my experiences by focusing on one hypothesis at a time and slowly accumulating what I consider to be informative observations and conclusions.

Compass Labs is a heavy user of Clojure for analytics and data process. We have been using Stuart Sierra’s excellent clojure-hadoop package for running a wide variety of algorithms derived from dozens of different Java libraries over our datasets on large Elastic MapReduce clusters.

The standard way to build a Jar for mapreduce is to pack all the libraries for a given package into a single jar and upload it to EMR. Unfortunately, building uberjars for Hadoop is a mallet when a small tap is needed.

We recently reached a point where the overhead of uploading large jars causes a noticeable slow down in our development cycle, especially when launching jobs on connections with limited upload bandwidth and with the slower uberjar creation of lein 1.4.

There are (at least) two solutions to this:

Build smaller jars by having projects with dependencies specific to a given job

Cache the dependencies on the cluster and send over your dependency list and pull the set you need into the Distributed Cache at job configuration time.

To allow us to continue to package all our job steps in a single jar, source tree and lein project, we opted for the latter solution which I will now describe.